Quote:
Originally Posted by dvd8n
Or just fish it out of the epub when it's added the first time 
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If it's always appearing with the brown book as the default cover then the image you're seeing when you open the book to read it is not properly labelled as the cover image. Just as a test randomly pick a couple of your books and open them with Edit Book. If it doesn't have a cover.xhtml or a cover.jpg then they're not properly marked and Calibre is not going to assume that the first jpg listed is the cover unless you tell it to assume that.
The bulk option to setting the first image as the cover is to select multiple books then on the bulk edit screen under Change Cover is the option to set from ebook files. I recommend doing this in batches of 100 or less while using the Cover Grid View so that you can double-check the right image is now set as the cover.